-
1
-
-
84879762989
-
-
rPlant: R interface to the iPlant discovery environment, R package version 1.2. Available at: [accessed 19 July 2012]
-
Banbury, B., Michels, K., Beaulieu, J.M. & O'Meara, B. (2012) rPlant: R interface to the iPlant discovery environment, R package version 1.2. Available at: http://CRAN.R-project.org/package=rPlant [accessed 19 July 2012].
-
(2012)
-
-
Banbury, B.1
Michels, K.2
Beaulieu, J.M.3
O'Meara, B.4
-
2
-
-
58149185141
-
Genbank
-
Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. & Sayers, E.W. (2009) Genbank. Nucleic Acids Research, 37, D26-D31.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Sayers, E.W.5
-
3
-
-
34047108602
-
The delayed rise of present-day mammals
-
Bininda-Emonds, O.R.P., Cardillo, M., Jones, K.E., Macphee, R.D.E., Beck, R.M.D., Grenyer, R., Price, S.A., Vos, R.A., Gittleman, J.L. & Purvis, A. (2007) The delayed rise of present-day mammals. Nature, 446, 507-512.
-
(2007)
Nature
, vol.446
, pp. 507-512
-
-
Bininda-Emonds, O.R.P.1
Cardillo, M.2
Jones, K.E.3
Macphee, R.D.E.4
Beck, R.M.D.5
Grenyer, R.6
Price, S.A.7
Vos, R.A.8
Gittleman, J.L.9
Purvis, A.10
-
4
-
-
84857171783
-
Measuring the distance between multiple sequence alignments
-
Blackburne, B.P. & Whelan, S. (2012) Measuring the distance between multiple sequence alignments. Bioinformatics, 28, 495-502.
-
(2012)
Bioinformatics
, vol.28
, pp. 495-502
-
-
Blackburne, B.P.1
Whelan, S.2
-
5
-
-
33645024781
-
Posterior mapping and posterior predictive distributions
-
Chap. 16 (ed. R. Neilsen) -, Springer, New York, NY.
-
Bollback, J. (2005) Posterior mapping and posterior predictive distributions. Statistical Methods in Molecular Evolution, Chap. 16 (ed. R. Neilsen ), pp. 439-462, Springer, New York, NY.
-
(2005)
Statistical Methods in Molecular Evolution
, pp. 439-462
-
-
Bollback, J.1
-
6
-
-
37849053471
-
Estimating divergence times in large phylogenetic trees
-
Britton, T., Anderson, C.L., Jacquet, D., Lundqvist, S. & Bremer, K. (2007) Estimating divergence times in large phylogenetic trees. Systematic Biology, 56, 741-752.
-
(2007)
Systematic Biology
, vol.56
, pp. 741-752
-
-
Britton, T.1
Anderson, C.L.2
Jacquet, D.3
Lundqvist, S.4
Bremer, K.5
-
7
-
-
67650757433
-
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
-
Capella-Gutiérrez, S., Silla-Martínez, J. & Gabaldón, T. (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25, 1972-1973.
-
(2009)
Bioinformatics
, vol.25
, pp. 1972-1973
-
-
Capella-Gutiérrez, S.1
Silla-Martínez, J.2
Gabaldón, T.3
-
8
-
-
66349134056
-
The merging of community ecology and phylogenetic biology
-
Cavender-Bares, J., Kozak, K., Fine, P.V.A. & Kembel, S.W. (2009) The merging of community ecology and phylogenetic biology. Ecology Letters, 12, 693-715.
-
(2009)
Ecology Letters
, vol.12
, pp. 693-715
-
-
Cavender-Bares, J.1
Kozak, K.2
Fine, P.V.A.3
Kembel, S.W.4
-
9
-
-
65649092976
-
Biopython: freely available python tools for computational molecular biology and bioinformatics
-
Cock, P.J.A., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B. & de Hoon, M.J.L. (2009) Biopython: freely available python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423.
-
(2009)
Bioinformatics
, vol.25
, pp. 1422-1423
-
-
Cock, P.J.A.1
Antao, T.2
Chang, J.T.3
Chapman, B.A.4
Cox, C.J.5
Dalke, A.6
Friedberg, I.7
Hamelryck, T.8
Kauff, F.9
Wilczynski, B.10
de Hoon, M.J.L.11
-
10
-
-
1242264357
-
Darwin's abominable mystery: insights from a supertree of the angiosperms
-
Davies, T.J., Barraclough, T.G., Chase, M.W., Soltis, P.S., Soltis, D.E. & Savolainen, V. (2004) Darwin's abominable mystery: insights from a supertree of the angiosperms. Proceedings of the National Academy of Sciences of the United States of America, 101, 1904-1909.
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, pp. 1904-1909
-
-
Davies, T.J.1
Barraclough, T.G.2
Chase, M.W.3
Soltis, P.S.4
Soltis, D.E.5
Savolainen, V.6
-
11
-
-
38649110663
-
BEAST: Bayesian evolutionary analysis by sampling trees
-
Drummond, A. & Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
-
(2007)
BMC Evolutionary Biology
, vol.7
, pp. 214
-
-
Drummond, A.1
Rambaut, A.2
-
12
-
-
33344465800
-
Relaxed phylogenetics and dating with confidence
-
Drummond, A.J., Ho, S.Y.W., Phillips, M.J. & Rambaut, A. (2006) Relaxed phylogenetics and dating with confidence. PLoS Biology, 4, e88.
-
(2006)
PLoS Biology
, vol.4
-
-
Drummond, A.J.1
Ho, S.Y.W.2
Phillips, M.J.3
Rambaut, A.4
-
13
-
-
84864530626
-
Bayesian phylogenetics with BEAUti and the BEAST 1.7
-
Drummond, A.J., Suchard, M.A., Xie, D. & Rambaut, A. (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29, 1969-1973.
-
(2012)
Molecular Biology and Evolution
, vol.29
, pp. 1969-1973
-
-
Drummond, A.J.1
Suchard, M.A.2
Xie, D.3
Rambaut, A.4
-
14
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792-1797.
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
15
-
-
0022203256
-
Phylogenies and the comparative method
-
Felsenstein, J. (1985) Phylogenies and the comparative method. The American Naturalist, 125, 1-15.
-
(1985)
The American Naturalist
, vol.125
, pp. 1-15
-
-
Felsenstein, J.1
-
18
-
-
83255165385
-
Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees
-
Izquierdo-Carrasco, F., Smith, S. & Stamatakis, A. (2011) Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees. BMC Bioinformatics, 12, 470.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 470
-
-
Izquierdo-Carrasco, F.1
Smith, S.2
Stamatakis, A.3
-
19
-
-
45949107473
-
Recent developments in the MAFFT multiple sequence alignment program
-
Katoh, K. & Toh, H. (2008) Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics, 9, 286-298.
-
(2008)
Briefings in Bioinformatics
, vol.9
, pp. 286-298
-
-
Katoh, K.1
Toh, H.2
-
20
-
-
13744252890
-
MAFFT version 5: improvement in accuracy of multiple sequence alignment
-
Katoh, K., Kuma, K.I., Toh, H. & Miyata, T. (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research, 33, 511-518.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.I.2
Toh, H.3
Miyata, T.4
-
21
-
-
80055110246
-
Estimating phylogenies for species assemblages: a complete phylogeny for the past and present native birds of New Zealand
-
Lanfear, R. & Bromham, L. (2011) Estimating phylogenies for species assemblages: a complete phylogeny for the past and present native birds of New Zealand. Molecular Phylogenetics and Evolution, 61, 958-963.
-
(2011)
Molecular Phylogenetics and Evolution
, vol.61
, pp. 958-963
-
-
Lanfear, R.1
Bromham, L.2
-
22
-
-
70350528406
-
-
Lemey, P., Salemi, M. & Vandamme, A.M. (eds). (), 2nd edn. Cambridge University Press, Cambridge.
-
Lemey, P., Salemi, M. & Vandamme, A.M. (eds). (2009) The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, 2nd edn. Cambridge University Press, Cambridge.
-
(2009)
The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing
-
-
-
23
-
-
84555194934
-
SATé-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees
-
Liu, K., Warnow, T.J., Holder, M.T., Nelesen, S.M., Yu, J., Stamatakis, A.P. & Linder, C.R. (2012) SATé-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Systematic Biology, 61, 90-106.
-
(2012)
Systematic Biology
, vol.61
, pp. 90-106
-
-
Liu, K.1
Warnow, T.J.2
Holder, M.T.3
Nelesen, S.M.4
Yu, J.5
Stamatakis, A.P.6
Linder, C.R.7
-
25
-
-
39149141072
-
AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in bayesian phylogenetics
-
Nylander, J.A.A., Wilgenbusch, J.C., Warren, D.L. & Swofford, D.L. (2008) AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in bayesian phylogenetics. Bioinformatics, 24, 581-583.
-
(2008)
Bioinformatics
, vol.24
, pp. 581-583
-
-
Nylander, J.A.A.1
Wilgenbusch, J.C.2
Warren, D.L.3
Swofford, D.L.4
-
27
-
-
80051801316
-
The taming of an impossible child: a standardized all-in approach to the phylogeny of hymenoptera using public database sequences
-
Peters, R., Meyer, B., Krogmann, L., Borner, J., Meusemann, K., Schutte, K., Niehuis, O. & Misof, B. (2011) The taming of an impossible child: a standardized all-in approach to the phylogeny of hymenoptera using public database sequences. BMC Biology, 9, 55.
-
(2011)
BMC Biology
, vol.9
, pp. 55
-
-
Peters, R.1
Meyer, B.2
Krogmann, L.3
Borner, J.4
Meusemann, K.5
Schutte, K.6
Niehuis, O.7
Misof, B.8
-
28
-
-
84879752840
-
-
Tracer v1.5. Available at: [Accessed 11 April 2013]
-
Rambaut, A. & Drummond, A. (2009) Tracer v1.5. Available at: http://beast.bio.ed.ac.uk/Tracer [Accessed 11 April 2013].
-
(2009)
-
-
Rambaut, A.1
Drummond, A.2
-
29
-
-
84866331426
-
Computing diversity from dated phylogenies and taxonomic hierarchies: does it make a difference to the conclusions?
-
Ricotta, C., Bacaro, G., Marignani, M., Godefroid, S. & Mazzoleni, S. (2012) Computing diversity from dated phylogenies and taxonomic hierarchies: does it make a difference to the conclusions? Oecologia, 170, 501-506.
-
(2012)
Oecologia
, vol.170
, pp. 501-506
-
-
Ricotta, C.1
Bacaro, G.2
Marignani, M.3
Godefroid, S.4
Mazzoleni, S.5
-
30
-
-
84874708221
-
Building megaphylogenies for macroecology: taking up the challenge
-
Roquet, C., Thuiller, W. & Lavergne, S. (2013) Building megaphylogenies for macroecology: taking up the challenge. Ecography, 36, 013-026.
-
(2013)
Ecography
, vol.36
, pp. 013-026
-
-
Roquet, C.1
Thuiller, W.2
Lavergne, S.3
-
31
-
-
80054078476
-
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
-
Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Soding, J., Thompson, J.D. & Higgins, D.G. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7, 529.
-
(2011)
Molecular Systems Biology
, vol.7
, pp. 529
-
-
Sievers, F.1
Wilm, A.2
Dineen, D.3
Gibson, T.J.4
Karplus, K.5
Li, W.6
Lopez, R.7
McWilliam, H.8
Remmert, M.9
Soding, J.10
Thompson, J.D.11
Higgins, D.G.12
-
32
-
-
60849123934
-
Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches
-
Smith, S.A., Beaulieu, J.M. & Donoghue, M.J. (2009) Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evolutionary Biology, 9, 37.
-
(2009)
BMC Evolutionary Biology
, vol.9
, pp. 37
-
-
Smith, S.A.1
Beaulieu, J.M.2
Donoghue, M.J.3
-
33
-
-
33750403801
-
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688-2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
34
-
-
84865083935
-
Bio.phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in biopython
-
Talevich, E., Invergo, B., Cock, P. & Chapman, B. (2012) Bio.phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in biopython. BMC Bioinformatics, 13, 209.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 209
-
-
Talevich, E.1
Invergo, B.2
Cock, P.3
Chapman, B.4
-
35
-
-
58849095783
-
Emerging patterns in the comparative analysis of phylogenetic community structure
-
Vamosi, S., Heard, S.B., Vamosi, C. & Webb, C.O. (2009) Emerging patterns in the comparative analysis of phylogenetic community structure. Molecular Ecology, 18, 572-592.
-
(2009)
Molecular Ecology
, vol.18
, pp. 572-592
-
-
Vamosi, S.1
Heard, S.B.2
Vamosi, C.3
Webb, C.O.4
-
36
-
-
14844350168
-
Phylomatic: tree assembly for applied phylogenetics
-
Webb, C.O. & Donoghue, M.J. (2005) Phylomatic: tree assembly for applied phylogenetics. Molecular Ecology Notes, 5, 181-183.
-
(2005)
Molecular Ecology Notes
, vol.5
, pp. 181-183
-
-
Webb, C.O.1
Donoghue, M.J.2
-
37
-
-
0036909621
-
Phylogenies and community ecology
-
Webb, C.O., Ackerly, D.D., McPeek, M.A. & Donoghue, M.J. (2002) Phylogenies and community ecology. Annual Review of Ecology and Systematics, 33, 475-505.
-
(2002)
Annual Review of Ecology and Systematics
, vol.33
, pp. 475-505
-
-
Webb, C.O.1
Ackerly, D.D.2
McPeek, M.A.3
Donoghue, M.J.4
-
38
-
-
51749095104
-
Phylocom: software for the analysis of phylogenetic community structure and trait evolution
-
Webb, C.O., Ackerly, D.D. & Kembel, S.W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics, 24, 2098-2100.
-
(2008)
Bioinformatics
, vol.24
, pp. 2098-2100
-
-
Webb, C.O.1
Ackerly, D.D.2
Kembel, S.W.3
-
39
-
-
0032028624
-
On the best evolutionary rate for phylogenetic analysis
-
Yang, Z. (1998) On the best evolutionary rate for phylogenetic analysis. Systematic Biology, 47, 125-133.
-
(1998)
Systematic Biology
, vol.47
, pp. 125-133
-
-
Yang, Z.1
|